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[bioontology-support] Missing metrics in HORD ontology

Laia Subirats laia.subirats at gmail.com
Thu Aug 17 03:32:07 PDT 2017


Dear Jennifer,

I would like to ask you help about this issue. I am still lost about how
can I solve this error.

Best,

Laia

On Tue, Aug 8, 2017 at 1:00 PM, Laia Subirats <laia.subirats at gmail.com>
wrote:

> Hello Jennifer,
>
> I change the imports. I uploaded the external ontologies in my Github
> webpage and pointed my ontology to them. I also changed the unamed.owl
> import.
>
> However, now I have this error: "(Uploaded, Error Rdf)".
>
> I have uploaded to webprotege and it works properly, and in my local
> Protégé as well.
>
> Sorry for making you spend time helping me.
>
> Best,
>
> Laia
> On Mon, Aug 7, 2017 at 6:46 PM, Jennifer Leigh Vendetti <
> vendetti at stanford.edu> wrote:
>
>> Hello Laia,
>>
>> I looked at your latest ontology source file
>> (HORD_all_2017_08_07_scenarios.owl). There are still a number of
>> problems with the import statements.
>>
>> 1). It’s not valid to use a BioPortal REST API call as a download URL for
>> the location of an ontology that you’d like to import. The import
>> statements on lines 21 and 23 in your ontology file will result in not
>> found errors:
>>
>> <owl:imports rdf:resource="http://data.bioontology.org/ontologies/ICF/
>> submissions/3/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688"/>
>>>> <owl:imports rdf:resource="http://data.bioontology.org/ontologies/ORDO/
>> submissions/11/download?apikey=eb8ef13c-ae88-42a5-b6f5-39c93d736688”/>
>>
>> This is true not only for BioPortal, but for other ontology editing
>> environments as well. If I open your ontology in the Protege ontology
>> editing environment [1], you will see errors for both of those imports:
>>
>>
>>
>>
>>
>> 2). Line 26 contains another invalid import statement:
>>
>> <owl:imports rdf:resource="http://www.owl-ontologies.com/unnamed.owl"/>
>>
>> … which has a URL that doesn’t resolve to anything.
>>
>> Kind regards,
>> Jennifer
>>
>> [1] http://protege.stanford.edu/products.php
>>
>>
>>
>> On Aug 6, 2017, at 10:21 PM, Laia Subirats <laia.subirats at gmail.com>
>> wrote:
>>
>> Hi John,
>>
>> I changed the references and now there is not a parsing problem anymore.
>> However, the metrics do not appear.
>>
>> Cheers,
>>
>> Laia Subirats
>> On Mon, Aug 7, 2017 at 1:40 AM, John Graybeal <jgraybeal at stanford.edu>
>> wrote:
>>
>>> Hi Laia,
>>>
>>> Sorry for the trouble you are having.  Usually that message indicates
>>> there has been a problem parsing the ontology, and you can try verifying
>>> the ontology parses with Protege or WebProtege as a next step.
>>>
>>> In this case, a quick look at the error log indicated two issues:
>>> * "OWL_IMPORT_MISSING: http://who.int/icf"
>>> * "OWL_IMPORT_MISSING: http://www.orpha.net/version2.4"
>>>
>>> A quick suggestion (sorry, no time today to verify myself) is to check
>>> to confirm that those two ontologies are indeed at those locations, and if
>>> they are not, change the references in the source ontology to point to
>>> correct locations.
>>>
>>> If you are still having trouble after that, please send another note
>>> indicating your latest understanding, and our team will try to help. Thanks.
>>>
>>> John
>>>
>>>
>>> On Aug 5, 2017, at 9:52 PM, Laia Subirats <laia.subirats at gmail.com>
>>> wrote:
>>>
>>> Dear Sir/Madam,
>>>
>>> I would like to see the metrics of my ontology in
>>> http://bioportal.bioontology.org/ontologies/HORD
>>> <http://bioportal.bioontology.org/ontologies/PMR>, I do not know if
>>> there is any problem. I see that there is a "(Uploaded, Error Rdf)" but
>>> I do not see the problem.
>>>
>>> Yours faithfully,
>>> --
>>> Laia Subirats
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>>
>>>
>>> ========================
>>> John Graybeal
>>> Technical Program Manager
>>> Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
>>> Stanford Center for Biomedical Informatics Research
>>>
>>
>>
>>
>> --
>> Laia Subirats
>> _______________________________________________
>> bioontology-support mailing list
>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>>
>>
>
>
> --
> Laia Subirats
>



-- 
Laia Subirats
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